82 Questions
What is the primary role of metal ions in some metalloproteins?
To play a purely structural role
What happens to the coordinated water molecules when metal ions bind to protein sites?
They are discarded
What is the significance of the large ionic radii of metal ions?
They can afford high coordination numbers
What is the importance of the formation of cross-links in some inorganic-element-based drugs?
It is crucial for the mechanism of action of the drugs
What is the role of the metal center in the enzyme aspartate transcarbamoylase (ATCase)?
To stabilize the structure of the enzyme
What is the result of the reaction catalyzed by aspartate transcarbamoylase (ATCase)?
The formation of carbamoyl aspartate plus inorganic phosphate
What is the effect of adding CTP to the enzyme aspartate transcarbamoylase?
It decreases enzyme activity
What is the function of the regulatory subunit in the holoenzyme?
It contains binding sites for inhibitors and activators
What is the result of partial disruption of the quaternary structure of the enzyme?
The catalytic and regulatory units separate
What is the role of the zinc ions in the holoenzyme?
They stabilize domains involved in interactions between the regulatory and catalytic subunits
What is the effect of an inhibitor on the enzyme's quaternary structure?
It shifts the equilibrium towards the T state
What is the structure of the native enzyme aspartate transcarbamoylase?
It has a D, symmetry
What is the result of modifying approximately 24 cysteine residues in the enzyme?
The six zinc ions are released from the holoenzyme
What is the function of the catalytic subunit in the holoenzyme?
It contains the active site for the enzyme
What is the effect of adding ATP to the enzyme aspartate transcarbamoylase?
It increases enzyme activity
What is the model that explains the allosteric behavior of ATCase?
The Monod-Wyman-Changeux model
What was the outcome of cleaving the cysteinate-mercury adducts with excess thiol?
Formation of apo-regulatory subunits that reassociate with the catalytic subunit only when zinc is added
What is the consequence of adding the zinc domain to the catalytic domains?
The affinity for aspartate becomes about twice that of the isolated catalytic domains
What is the role of zinc in transcription factor IIIA (TFIIIA)?
Zinc is essential for specific binding to DNA
What is the characteristic feature of the nine tandem sequences in TFIIIA?
They have a repetitive sequence of cysteines and histidines
What is the proposed structure of each of the nine sequences in TFIIIA?
A zinc-binding domain organized around a zinc ion bound to the invariant cysteine and histidine residues
What is the effect of removing zinc from TFIIIA on its DNA-binding activity?
It abolishes DNA-binding activity
What is the role of the zinc domain in the regulatory subunit?
It allows formation of a small protein domain that binds to the catalytic subunit in a manner that produces conversion from a T-like to an R-like state
What is the stoichiometry of the complex formed between the zinc domain and the catalytic trimer?
3:1
What is the effect of adding zinc to the TFIIIA-5S RNA complex after EDTA treatment?
It restores specific binding activity
What is the number of zinc ions bound to each TFIIIA protein?
7-11
What is the term given to the domains in the proposed structure?
Zinc fingers
What technique was used to probe the nature of the ligands coordinated to the zinc ions?
EXAFS spectroscopy
What is the distance of the sulfur atoms from the zinc ion in the EXAFS spectra?
2.30 A
What is the ion that binds to the peptide corresponding to the second zinc-finger domain of TFIIIA?
Zn2+
What is the shape of the coordination in the cobalt complex?
Tetrahedral
What is the effect of adding zinc ions to the peptide on its susceptibility to cleavage by trypsin?
It decreases its susceptibility
What is the relative affinity of Zn2+ compared to other ions?
103-105 times more tightly
What is the estimated number of genes in the human genome that encode zinc-finger domains?
500
What is the range of domains in a single protein?
1-37
What is the effect of adding zinc ions to the peptide on its structure?
It induces a well-ordered structure
What is the common feature among the zinc finger proteins shown in Figure 7.4?
The number of zinc finger domains
What is the approximate diameter of each virus particle capsid?
50 nm
What is the role of zinc binding in the protein classes discussed in the text?
To induce structural changes and stabilization
What is the coordination of zinc in a zinc finger domain?
Two cysteinate and two histidine residues
What is the potential role of zinc in gene-regulatory networks?
Both as a structural device and an information carrier or messenger
What is the consequence of the structure of a zinc finger domain?
The amino and carboxyl termini are far from each other
What is the function of calmodulin in signal transduction pathways?
To sense changes in intracellular calcium concentrations
What is the organization of the cysteines in the steroid receptor superfamily?
Two units of four cysteine residues each
What is the role of one of the zinc-based units in the steroid receptor superfamily?
Dimerization of the protein
How many Ca2+ ions can calmodulin bind?
Four
What was the discovery that led to the identification of zinc in GAL4?
A yeast strain with a mutant GAL4 gene
What is the term for the calcium-binding structure in calmodulin?
EF hand
What is the coordination number of each calcium ion in the EF-hand unit?
Seven
What is the configuration of the proline residue in the GAL4 protein?
Cis peptide bond
What is the function of the retroviral nucleocapsid proteins?
Retroviral replication
What is the nature of the residues that bind to calcium in the EF-hand unit?
Negatively charged
What is the significance of the paired EF-hand domains in calmodulin?
The two members of a pair pack against each other via nonpolar residues
What has been demonstrated by EXAFS experiments on retroviral nucleocapsid proteins?
The presence of zinc inside intact retrovirus particles
What has been revealed by NMR studies on zinc finger domains?
The three-dimensional structure of the domains
What is the consequence of zinc binding in nucleic acid-binding proteins?
Induction of structural changes and stabilization
What is the key factor that favors Ca2+ binding over Mg2+ binding in EF-hand sites?
The smaller size of Mg2+ ions
What is the range of dissociation constants for Ca2+ binding to calmodulin?
1 nM to 1 μM
What is the shape of the calmodulin molecule?
Dumbbell-shaped
What type of structures do the regions responsible for calmodulin binding tend to form?
Alpha-helical structures
What is the purpose of the hydrophobic patches on the surface of the calmodulin lobes?
To facilitate binding to target molecules
What is the characteristic feature of the long alpha helix in calmodulin?
It is stabilized by salt bridges
What is the typical dissociation constant for calmodulin binding to its targets?
1 nM to 1 μM
What is the effect of calmodulin binding to its target molecules?
It enhances the activity of the target molecule
What is the role of the E and F helices in the EF-hand domain?
They form the calcium-binding site
What is the significance of the seven calcium-bound oxygen atoms in the EF-hand domain?
They are derived from amino acid side chains and the peptide backbone
What is the role of calcium in cellular processes?
It binds to calmodulin, leading to conformational changes and target activation
What is the function of membrane-permeable fluorescent calcium-binding dyes like Fura-2?
To measure the changes in intracellular calcium concentration
What is the effect of adding phenylephrine to cells from a vascular smooth muscle cell line?
It increases intracellular calcium levels to approximately 0.5 millimolar
What is the role of counterions in nucleic acid structure?
To neutralize the negatively charged phosphate groups
What is the effect of increasing intracellular calcium concentration on calmodulin?
It increases the binding of calcium to calmodulin, leading to conformational changes
What is the significance of the increase in intracellular calcium levels in response to phenylephrine treatment?
It is a signaling event that can activate specific cellular processes
What is the significance of methionine residues in the hydrophobic patches of calmodulin?
They contribute nearly 50 percent of the accessible surface
What is the result of the binding of calcium to calmodulin?
It induces conformational changes in the protein
What is the role of the central helix in calmodulin?
It is unwound to form a bend upon target peptide binding
What is the characteristic feature of the peptides that bind to calmodulin?
They have a specific sequence motif
What is the function of the two lobes of calmodulin?
They interact with target peptides
What is the outcome of the binding of target peptides to calmodulin?
The target peptide is encapsulated
What is the role of the hydrophobic surfaces on the two calcium-binding lobes of calmodulin?
They interact with target peptides
What is the significance of the flexibility of the connecting helix in calmodulin?
It enables the binding of target peptides
What is the outcome of the structural studies of the calmodulin-target peptide complexes?
The complexes have approximate twofold symmetry
What is the significance of the analysis of the calmodulin complex with a 26-residue peptide from skeletal-muscle myosin light-chain kinase?
It demonstrated the use of newly developed NMR methods
Understand how metals interact with biological molecules, including proteins and nucleic acids, to influence their structure and function. Learn about the role of metal binding in inducing tertiary structures and facilitating interactions between macromolecules.
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